<?xml version="1.0"?>
<doc>
    <assembly>
        <name>NAligner</name>
    </assembly>
    <members>
        <member name="T:NAligner.Formats.FASTA">
            <summary> <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> formatter</summary>
        </member>
        <member name="T:NAligner.Formats.AlignmentFormatter">
            <summary> Abstract format </summary>
        </member>
        <member name="F:NAligner.Formats.AlignmentFormatter.id">
            <summary> Formatter id </summary>
        </member>
        <member name="M:NAligner.Formats.AlignmentFormatter.Format(NAligner.PairwiseAlignment)">
            <summary> Formats alignment</summary>
            <returns> formatted alignment </returns>
        </member>
        <member name="P:NAligner.Formats.AlignmentFormatter.Id">
            <summary> Gets or sets format id</summary>
        </member>
        <member name="F:NAligner.Formats.FASTA.LINE_WIDTH">
            <summary> Number of characters per line</summary>
        </member>
        <member name="M:NAligner.Formats.FASTA.#ctor">
            <summary> Constructor for FASTA.</summary>
        </member>
        <member name="M:NAligner.Formats.FASTA.Format(NAligner.Sequence)">
            <summary> Returns the name, description and sequence combined in one string.
            The length of each line in the sequence is FASTA.LINE_LENGTH</summary>
        </member>
        <member name="M:NAligner.Formats.FASTA.Format(NAligner.PairwiseAlignment)">
            <returns> FASTA format of the input alignment</returns>
        </member>
        <member name="T:NAligner.Markups">
            <summary> Markups line characters. </summary>
        </member>
        <member name="F:NAligner.Markups.IDENTITY">
            <summary> Markup line identity character</summary>
        </member>
        <member name="F:NAligner.Markups.SIMILARITY">
            <summary> Markup line similarity character</summary>
        </member>
        <member name="F:NAligner.Markups.GAP">
            <summary> Markup line gap character</summary>
        </member>
        <member name="F:NAligner.Markups.MISMATCH">
            <summary> Markup line mismatch character</summary>
        </member>
        <member name="T:NAligner.PairwiseAlignment">
            <summary> Holds the output of a pairwise sequences alignment. </summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.GAP">
            <summary> Gap character</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.DEFAULT_SEQUENCE1_NAME">
            <summary> Default name for sequence #1</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.DEFAULT_SEQUENCE2_NAME">
            <summary> Default name for sequence #2</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.matrix">
            <summary> Scoring matrix</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.open">
            <summary> Gap open cost</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.extend">
            <summary> Gap extend cost</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.score">
            <summary> Alignment score</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.sequence1">
            <summary> Aligned sequence #1</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.name1">
            <summary> Name of sequence #1</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.start1">
            <summary> Alignment start location in sequence #1</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.sequence2">
            <summary> Aligned sequence #2</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.name2">
            <summary> Name of sequence #2</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.start2">
            <summary> Alignment start location in sequence #2</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.markupLine">
            <summary> Markup line</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.identity">
            <summary> Count of identical locations</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.similarity">
            <summary> Count of similar locations</summary>
        </member>
        <member name="F:NAligner.PairwiseAlignment.gaps">
            <summary> Count of gap locations</summary>
        </member>
        <member name="M:NAligner.PairwiseAlignment.#ctor">
            <summary> Constructor for Alignment</summary>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Extend">
            <returns> Returns the extend. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Matrix">
            <returns> Returns the matrix. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Name1">
            <returns> Returns the name1. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Name2">
            <returns> Returns the name2. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Open">
            <returns> Returns the open. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Score">
            <returns> Returns the score. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Sequence1">
            <returns> Returns the sequence1. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Sequence2">
            <returns> Returns the sequence2. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Start1">
            <returns> Returns the start1. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Start2">
            <returns> Returns the start2. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Gaps">
            <returns> Returns the gaps. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Identity">
            <returns> Returns the identity. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.MarkupLine">
            <returns> Returns the markupLine. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Similarity">
            <returns> Returns the similarity. </returns>
        </member>
        <member name="P:NAligner.PairwiseAlignment.Summary">
            <summary> Returns a summary for alignment</summary>
        </member>
        <member name="T:NAligner.Utils.AlphanumericComparator">
            <summary> Comparator to sort the scoring matrices by their names. </summary>
        </member>
        <member name="M:NAligner.Utils.AlphanumericComparator.FirstDigitIndex(System.String)">
            <summary> Returns the index of the first digit in a String.
            If there are no digits, returns -1.</summary>
        </member>
        <member name="T:NAligner.Cell">
            <summary> A cell in a similarity matrix, to hold row, column and score.</summary>
        </member>
        <member name="F:NAligner.Cell.row">
            <summary> Row of the cell</summary>
        </member>
        <member name="F:NAligner.Cell.column">
            <summary> Column of the cell</summary>
        </member>
        <member name="F:NAligner.Cell.score">
            <summary> Alignment score at this cell</summary>
        </member>
        <member name="M:NAligner.Cell.#ctor">
            <summary> Constructor</summary>
        </member>
        <member name="M:NAligner.Cell.Set(System.Int32,System.Int32,System.Single)">
            <summary> Sets the row, column and score of the cell.</summary>
        </member>
        <member name="P:NAligner.Cell.Column">
            <summary> Gets or sets the column. </summary>
        </member>
        <member name="P:NAligner.Cell.Row">
            <summary>Gets or sets the row.</summary>
        </member>
        <member name="P:NAligner.Cell.Score">
            <summary>Gets or sets the score.</summary>
        </member>
        <member name="T:NAligner.Directions">
            <summary> Traceback directions. </summary>
        </member>
        <member name="F:NAligner.Directions.STOP">
            <summary> Traceback direction stop</summary>
        </member>
        <member name="F:NAligner.Directions.LEFT">
            <summary> Traceback direction left</summary>
        </member>
        <member name="F:NAligner.Directions.DIAGONAL">
            <summary> Traceback direction diagonal</summary>
        </member>
        <member name="F:NAligner.Directions.UP">
            <summary> Traceback direction up</summary>
        </member>
        <member name="T:NAligner.Utils.NAlignerException">
            <summary> JAligner exception </summary>
        </member>
        <member name="T:NAligner.Formats.NamespaceDoc">
            <summary>Group of formats for output alignments.</summary>
        </member>
        <member name="T:NAligner.Formats.Pair">
            <summary>
            <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.</summary>
        </member>
        <member name="F:NAligner.Formats.Pair.NAME_WIDTH">
            <summary> Name width </summary>
        </member>
        <member name="F:NAligner.Formats.Pair.POSITION_WIDTH">
            <summary> Position width</summary>
        </member>
        <member name="F:NAligner.Formats.Pair.SEQUENCE_WIDTH">
            <summary> Sequence width</summary>
        </member>
        <member name="F:NAligner.Formats.Pair.BLANK">
            <summary> Space</summary>
        </member>
        <member name="M:NAligner.Formats.Pair.#ctor">
            <summary> Constructor </summary>
        </member>
        <member name="M:NAligner.Formats.Pair.Format(NAligner.PairwiseAlignment)">
            <summary> Formats an alignment object to the Pair_FORMAT format</summary>
            <param name="alignment">alignment object to be formated </param>
            <returns> string of the alignment pair-formatted </returns>
        </member>
        <member name="T:NAligner.Utils.Commons">
            <summary> Global constants and varilables  </summary>
        </member>
        <member name="F:NAligner.Utils.Commons.CURRENT_RELEASE">
            <summary> Current release version of JAligner</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.DEFAULT_USER_DIRECTORY">
            <summary> Default home directory</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.DEFAULT_FILE_SEPARATOR">
            <summary> Default file separator</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.DEFAULT_LINE_SEPARATOR">
            <summary> Default line separator</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.userDirectory">
            <summary> User home directory</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.fileSeparator">
            <summary> Line separator</summary>
        </member>
        <member name="F:NAligner.Utils.Commons.lineSeparator">
            <summary> Line separator</summary>
        </member>
        <member name="P:NAligner.Utils.Commons.FileSeparator">
            <summary> Returns system file separator.</summary>
            <returns> file separator </returns>
        </member>
        <member name="P:NAligner.Utils.Commons.LineSeparator">
            <summary> Returns system line separator.</summary>
            <returns> line separator </returns>
        </member>
        <member name="P:NAligner.Utils.Commons.UserDirectory">
            <summary> Returns user's current directory.</summary>
            <returns> user's current directory </returns>
        </member>
        <member name="P:NAligner.Utils.Commons.CurrentRelease">
            <summary> Returns the current release version of JAligner</summary>
        </member>
        <member name="T:NAligner.NamespaceDoc">
            <summary>
            <h3>NAligner</h3>
            <p>Implementation of Smith-Waterman-Gotoh algorithm.</p>
            <p>NAligner is a port of <a href="http://jaligner.sourceforge.net">JAligner</a>.</p>
            <p/>
            <p>Original author: Ahmed Moustafa (ahmed@users.sf.net).</p>
            <p>.Net port by <a href="http://www.vermorel.com">Joannes Vermorel</a>.</p>
            </summary>
        </member>
        <member name="T:NAligner.Utils.Tokenizer">
            <summary>The class performs token processing in strings</summary>
            <remarks>Class create by the Java Language Conversion Assistant.</remarks>
        </member>
        <member name="F:NAligner.Utils.Tokenizer.currentPos">
            Position over the string
        </member>
        <member name="F:NAligner.Utils.Tokenizer.includeDelims">
            Include demiliters in the results.
        </member>
        <member name="F:NAligner.Utils.Tokenizer.chars">
            Char representation of the String to tokenize.
        </member>
        <member name="M:NAligner.Utils.Tokenizer.#ctor(System.String)">
            <summary>
            Initializes a new class instance with a specified string to process
            </summary>
            <param name="source">String to tokenize</param>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.#ctor(System.String,System.String)">
            <summary>
            Initializes a new class instance with a specified string to process
            and the specified token delimiters to use
            </summary>
            <param name="source">String to tokenize</param>
            <param name="delimiters">String containing the delimiters</param>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.#ctor(System.String,System.String,System.Boolean)">
            <summary>
            Initializes a new class instance with a specified string to process, the specified token
            delimiters to use, and whether the delimiters must be included in the results.
            </summary>
            <param name="source">String to tokenize</param>
            <param name="delimiters">String containing the delimiters</param>
            <param name="includeDelims">Determines if delimiters are included in the results.</param>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.NextToken">
            <summary>
            Returns the next token from the token list
            </summary>
            <returns>The string value of the token</returns>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.NextToken(System.String)">
            <summary>
            Returns the next token from the source string, using the provided
            token delimiters
            </summary>
            <param name="delimiters">String containing the delimiters to use</param>
            <returns>The string value of the token</returns>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.HasMoreTokens">
            <summary>
            Determines if there are more tokens to return from the source string
            </summary>
            <returns>True or false, depending if there are more tokens</returns>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.MoveNext">
            <summary>
             Performs the same action as HasMoreTokens.
            </summary>
            <returns>True or false, depending if there are more tokens</returns>
        </member>
        <member name="M:NAligner.Utils.Tokenizer.Reset">
            <summary>
            Does nothing.
            </summary>
        </member>
        <member name="P:NAligner.Utils.Tokenizer.Count">
            <summary>
            Remaining tokens count
            </summary>
        </member>
        <member name="P:NAligner.Utils.Tokenizer.Current">
            <summary>
             Performs the same action as NextToken.
            </summary>
        </member>
        <member name="T:NAligner.Formats.FormatterFactory">
            <summary> Singleton formatter factory. </summary>
        </member>
        <member name="F:NAligner.Formats.FormatterFactory.formats">
            <summary>Table containing the <see cref="T:NAligner.Formats.AlignmentFormatter"/>s.</summary>
        </member>
        <member name="M:NAligner.Formats.FormatterFactory.#ctor">
            <summary> Hidden constructor </summary>
        </member>
        <member name="M:NAligner.Formats.FormatterFactory.RegisterFormatter(NAligner.Formats.AlignmentFormatter)">
            <summary> Registers a new formatter.</summary>
        </member>
        <member name="M:NAligner.Formats.FormatterFactory.GetFormatter(System.String)">
            <summary> Returns a <see cref="T:NAligner.Formats.AlignmentFormatter"/>.</summary>
            <param name="id">formatter id </param>
        </member>
        <member name="P:NAligner.Formats.FormatterFactory.Default">
            <summary> Returns the singleton instance for <see cref="T:NAligner.Formats.FormatterFactory"/>.</summary>
        </member>
        <member name="P:NAligner.Formats.FormatterFactory.Formatters">
            <summary> Returns a list of registered formatters</summary>
        </member>
        <member name="T:NAligner.Sequence">
            <summary> A basic (nucleic or protein) sequence. It's a
            wrapper to <c>string</c>. </summary>
            <remarks>The <see cref="T:NAligner.Sequence"/> can be parsed if encoded with
            <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a>.</remarks>
        </member>
        <member name="F:NAligner.Sequence.aalist">
            <summary> List of amino acids</summary>
        </member>
        <member name="F:NAligner.Sequence.id">
            <summary> Sequence id.</summary>
        </member>
        <member name="F:NAligner.Sequence.description">
            <summary> Sequence description.</summary>
        </member>
        <member name="F:NAligner.Sequence.type">
            <summary> Sequence type.</summary>
        </member>
        <member name="M:NAligner.Sequence.#ctor">
            <summary> Constructor</summary>
        </member>
        <member name="M:NAligner.Sequence.#ctor(System.String,System.String,System.String,NAligner.SequenceType)">
            <summary> Constructor</summary>
        </member>
        <member name="M:NAligner.Sequence.Subsequence(System.Int32,System.Int32)">
            <summary> Returns a subsequence</summary>
            <param name="index">start index </param>
            <param name="length">length of subsequence </param>
            <returns> subsequence </returns>
        </member>
        <member name="M:NAligner.Sequence.AcidAt(System.Int32)">
            <summary> Returns the acid at specific location in the sequence</summary>
            <param name="index">index </param>
            <returns> acid at index </returns>
        </member>
        <member name="M:NAligner.Sequence.ToArray">
            <summary> Returns the sequence as an array of characters.</summary>
        </member>
        <member name="M:NAligner.Sequence.Parse(System.String)">
            <summary> Returns a parsed Sequence from a FASTA string.</summary>
            <param name="stringToParse">FASTA string to parse</param>
        </member>
        <member name="M:NAligner.Sequence.Parse(System.IO.FileInfo)">
            <summary> Returns a <see cref="T:NAligner.Sequence"/> parsed and loaded from a file</summary>
            <param name="file">to parse </param>
            <returns> parsed sequence  </returns>
        </member>
        <member name="M:NAligner.Sequence.PrepareAndValidate(System.String)">
            <summary> Removes whitespaces from a sequence and validates other characters.</summary>
            <param name="stringToParse">sequence to be prepared</param>
            <returns> prepared array of characters </returns>
        </member>
        <member name="P:NAligner.Sequence.Id">
            <summary> Returns the sequence id</summary>
        </member>
        <member name="P:NAligner.Sequence.Description">
            <summary> Returns the sequence description</summary>
        </member>
        <member name="P:NAligner.Sequence.Type">
            <summary> Returns the sequence type (nucleic or protein) </summary>
        </member>
        <member name="P:NAligner.Sequence.AAList">
            <summary> Gets or sets the amino acid sequence</summary>
        </member>
        <member name="T:NAligner.Formats.CLUSTAL">
             <summary> <p>CLUSTAL format.</p>
             Example:
             <code>
             CLUSTAL_FORMAT W(1.60) multiple sequence alignment
            
            
             JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
             KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
             FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
            
            
             JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
             KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
             FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
            
            
             JC2395          IAEEIQAM
             KPEL_DROME      AMRLIKDY
             FASA_MOUSE      TLDKFQDM
             </code>
            
             </summary>
             <author>  Ahmed Moustafa (ahmed@users.sf.net) </author>
        </member>
        <member name="F:NAligner.Formats.CLUSTAL.NAME_WIDTH">
            <summary> Name width </summary>
        </member>
        <member name="F:NAligner.Formats.CLUSTAL.SEQUENCE_WIDTH">
            <summary> Sequence width</summary>
        </member>
        <member name="F:NAligner.Formats.CLUSTAL.HEADER">
            <summary> CLUSTAL header</summary>
        </member>
        <member name="M:NAligner.Formats.CLUSTAL.#ctor">
            <summary> Constructor</summary>
        </member>
        <member name="M:NAligner.Formats.CLUSTAL.Format(System.String[],System.String[])">
            <summary> Returns CLUSTAL format</summary>
            <param name="names">array of the names of the sequences.</param>
            <param name="sequences">array of the sequences</param>
        </member>
        <member name="M:NAligner.Formats.CLUSTAL.Format(NAligner.PairwiseAlignment)">
            <summary> Returns CLUSTAL format of the alignment</summary>
        </member>
        <member name="T:NAligner.SmithWatermanGotoh">
            <summary> An implementation of the Smith-Waterman algorithm with
            Gotoh's improvement for biological local pairwise sequence alignment. </summary>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.#ctor">
            <summary> Hidden constructor</summary>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.Align(NAligner.Sequence,NAligner.Sequence,NAligner.ScoringMatrix,System.Single,System.Single)">
            <summary> Aligns two sequences by Smith-Waterman algorithm</summary>
            <param name="s1">sequene #1 </param>
            <param name="s2">sequene #2 </param>
            <param name="matrix">scoring matrix </param>
            <param name="o">open gap penalty </param>
            <param name="e">extend gap penalty </param>
            <returns> alignment object contains the two aligned sequences,
            the alignment score and alignment statistics</returns>
            <seealso cref="T:NAligner.Sequence"/>
            <seealso cref="!:Matrix"/>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.Construct(NAligner.Sequence,NAligner.Sequence,System.Single[0:,0:],System.Single,System.Single,System.Byte[],System.Int16[],System.Int16[])">
            <summary> Constructs directions matrix for the traceback </summary>
            <param name="s1">sequence #1 </param>
            <param name="s2">sequence #2 </param>
            <param name="matrix">scoring matrix </param>
            <param name="o">open gap penalty </param>
            <param name="e">extend gap penalty </param>
            <returns> The cell where the traceback starts. </returns>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.Traceback(NAligner.Sequence,NAligner.Sequence,NAligner.ScoringMatrix,System.Byte[],NAligner.Cell,System.Int16[],System.Int16[])">
            <summary> Returns the alignment of two sequences based on the passed array of pointers</summary>
            <param name="s1">sequence #1 </param>
            <param name="s2">sequence #2 </param>
            <param name="m">scoring matrix </param>
            <param name="cell">The cell where the traceback starts. </param>
            <returns> <see cref="!:Alignment"/> with the two aligned sequences and alignment score. </returns>
            <seealso cref="T:NAligner.Cell"/>
            <seealso cref="!:Alignment"/>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.Max(System.Single,System.Single,System.Single,System.Single)">
            <summary> Returns the maximum of 4 float numbers.</summary>
        </member>
        <member name="M:NAligner.SmithWatermanGotoh.Reverse(System.Char[],System.Int32)">
            <summary> Reverses an array of chars</summary>
        </member>
        <member name="T:NAligner.ScoringMatrix">
            <summary> Scoring matrix. </summary>
        </member>
        <member name="F:NAligner.ScoringMatrix.COMMENT_STARTER">
            <summary> The starter character of a comment line.</summary>
        </member>
        <member name="F:NAligner.ScoringMatrix.SIZE">
            <summary> The size of the scoring matrix. It is the number of the
            characters in the ASCII table. It is more than the 20 amino acids just
            to save the processing time of the mapping.</summary>
        </member>
        <member name="F:NAligner.ScoringMatrix.id">
            <summary> Matrix id (or name)</summary>
        </member>
        <member name="F:NAligner.ScoringMatrix.scores">
            <summary> Scores</summary>
        </member>
        <member name="M:NAligner.ScoringMatrix.Load(System.String)">
            <summary> Loads scoring matrix resource.</summary>
            <returns> loaded matrix </returns>
        </member>
        <member name="M:NAligner.ScoringMatrix.GetScore(System.Char,System.Char)">
            <returns> score </returns>
        </member>
        <member name="P:NAligner.ScoringMatrix.Id">
            <returns> Returns the id. </returns>
        </member>
        <member name="P:NAligner.ScoringMatrix.Scores">
            <returns> Returns the scores. </returns>
        </member>
    </members>
</doc>
